Theoretical and computational biophysics

The field of research is biophysics of macromolecules. The main results are related to the study of physical mechanisms of complex formation of active molecules and metal ions with the DNA and proteins. The phylosophy of research is to breadge the results of computational modeling with the experimental studies using the models of theoretical physics.

Cooperation

• Університет імені Павла Йозефа Шафарика в Кишицях (Словаччина)
• Університет Кальярі (Кальярі, Італія)

Graduate topics

• Terahertz dynamics of water molecules and counterions in the hydrated shell of the DNA double helix.
• Conformational dynamics of natural polyamines interacting with the DNA double helix.
• Dynamics of DNA in the condensed state and in the conditions of the viral capsid.
• Formation of stable complexes of drug molecules with DNA.
• Structure and dynamics of DNA in the nucleosome.
• Structure and dynamics of nanowires based on metallized DNA.
• DNA in an external electric field.
• Conformational mechanics of special forms of DNA and RNA.

Selected scientific publications

• Vasiliu T. , Mocci F., Laaksonen A., Engelbrecht L., Perepelytsya S., Caging polycations: Effect of increasing confinement on the modes of interaction of spermidine3+ with DNA double helices, Frontiers in Chemistry (2022). https://doi.org/10.3389/fchem.2022.836994
• Perepelytsya S. , Uličný J., Volkov S.N., Molecular Dynamics Study of the Competitive Binding of Hydrogen Peroxide and Water Molecules with DNA Phosphate Groups, Eur. Biophys. J. 50, 759 (2021). DOI: 10.1007/s00249-021-01522-8
• Zdorevskyi O.O., Perepelytsya S.M. Dynamics of K+ counterions around DNA double helix in the external electric field: a molecular dynamics study. Eur. Phys. J. E 43: 77, (2020). doi: 10.1140/epje/i202
• Perepelytsya S., Uličný J., Laaksonen A., Mocci F. Pattern preferences of DNA nucleotide motifs by polyamines putrescine2+, spermidine3+ and spermine4+. Nucleic Acids Research. 47, 6084 (2019).
• Perepelytsya S. Hydration of counterions interacting with DNA double helix: a molecular dynamics study. J. Molecular Modeling, 24, 171 (2018).
• Perepelytsya S.M., Volkov S.N. Conformational vibrations of ionic lattice in DNA: Manifestation in the low-frequency Raman spectra. J. Mol. Liq. 164, 113-119 (2011).
• Perepelytsya S.M., Volkov S.N.. Intensities of DNA ion-phosphate modes in low-frequency Raman spectra. Eur. Phys. J. E 31, 201-205 (2010).
• Perepelytsya S.M., Volkov S.N. Counterion vibrations in the DNA low-frequency spectra. Eur. Phys. J. E 24, 261-269 (2007).
• Bulavin L.A., Volkov S.N., Kutuvy S.Yu., Perepelytsya S.M.. Observation of the DNA ion-phosphate vibrations. Reports of National Academy of Science of Ukraine 11, 69-73 (2007).